Introduction

< Explain >

Goals

< what are you trying to achieve >


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Learn how to communicate with cbioportal and study what is available.

Find you TCGA ID

  • Important here: you need to replace this with your own assigned TCGA ID. For this report I’m using TCGA-AR-A24T

Clinical data.

Now that we have a basic understanding of what is available lets go and download the actual data.

mutation table

Identifying pathogenic mutations. <— need to redo with mt from here onwards

Now that the data has been succesfully donwloaded and annotated lets study it a bit more.

Besides Mutation data we also downloaded expression RNAseq data in the form of TPM.

demo only

  • Please see assignmet.
  • Figure out what figures to put and what to leave out.
  • know your myid and where it all fits.

RNAseq Volcano

Heatmap

GSEA summary1

GO 1

GO 2

mutations

CNA